Research workbench
Human diabetogenic TCR T1D3 in complex with DQ8-P8E9E peptide
Analyse Human diabetogenic TCR T1D3 in complex with DQ8-P8E9E peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DFX
- Type
- protein
- Length
- 1,615 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class II HLA-dq-alpha chain; MHC class II antigen; T1D3 alpha chain; T1D3 beta chain
- UniProt
- Q30069, U3PYM0
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | MHC class II HLA-dq-alpha chain | protein | 180 | 15% helix, 44% strand | Q30069 |
| B | MHC class II antigen | protein | 200 | 18% helix, 39% strand | U3PYM0 |
| E | MHC class II antigen | protein | 199 | 18% helix, 40% strand | U3PYM0 |
| G | T1D3 alpha chain | protein | 194 | 3% helix, 44% strand | — |
| H, J | T1D3 beta chain | protein | 237 | 7% helix, 52% strand | — |
| I | T1D3 alpha chain | protein | 188 | 4% helix, 41% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, D
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 946 | 0.75 | 0.78 | 80 | empty |
| 2 | 625 | 0.70 | 0.78 | 59 | empty |
| 3 | 874 | 0.69 | 0.75 | 82 | empty |
| 4 | 215 | 0.57 | 0.79 | 30 | empty |
| 5 | 283 | 0.56 | 0.77 | 44 | empty |
Interfaces
16 interfaces between chains.
- A–B · 3241 Ų buried · 76 hydrogen bonds · protein-protein
- D–E · 3188 Ų buried · 69 hydrogen bonds · protein-protein
- G–H · 2309 Ų buried · 37 hydrogen bonds · protein-protein
- I–J · 2182 Ų buried · 37 hydrogen bonds · protein-protein
- B–E · 681 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6DFX · human diabetogenic TCR T1D3 in complex with DQ8-p8E9E peptide · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q30069
- Every structure of UniProt U3PYM0
- Elsewhere: RCSB PDB 6DFX · PDBe 6DFX · UniProt Q30069 · UniProt U3PYM0
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